Merge remote-tracking branch 'remotes/trunk/develop' into develop

.github/workflows/gh-pages.yml

@@ -0,0 +1,88 @@
+name: Deploy documentation with GitHub Pages dependencies preinstalled
+
+on:
+  push:
+    branches: ["develop"]
+  workflow_dispatch: # enable manual workflow execution
+
+# Set permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    # prevent this action from running on forks
+    if: github.repository == 'abinit/abipy'
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - os: ubuntu-latest
+            python: '3.11'
+
+    runs-on: ubuntu-latest
+    env:
+      PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
+      # This is used in the flow scripts to generate the graph with graphviz.
+      READTHEDOCS: 1
+
+    steps:
+      - name: Check out Abipy repo
+        uses: actions/checkout@v4
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+            auto-update-conda: true
+
+      - name: Installing abinit from conda-forge and abipy with python=${{ matrix.config.python }}
+        run: |
+            conda create -n abipy python=${{ matrix.config.python }} --yes
+            conda activate abipy
+            conda install abinit -c conda-forge --yes
+            mpirun -n 1 abinit --version
+            mpirun -n 1 abinit --build
+            pip install --editable .
+            mkdir -p $HOME/.abinit/abipy/
+            cp abipy/data/managers/gh_manager.yml $HOME/.abinit/abipy/manager.yml
+            cp abipy/data/managers/gh_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
+            # FIXME TEMPORARY HACK
+            #pip install git+https://github.com/gmatteo/pymatgen.git@master -U
+
+      - name: Build docs with Sphinx
+        run: |
+            conda activate abipy
+            cd docs
+            source install.sh
+            make
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
+        with:
+          path: docs/_build/html/ # Important. Set to the website output dir
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v3

.github/workflows/test.yml

@@ -0,0 +1,72 @@
+name: Run the Abipy test suite.
+
+on:
+  push:
+    branches: [develop, master]
+    paths-ignore: ["**/*.md", docs/**]
+  pull_request:
+    branches: [develop]
+    paths-ignore: ["**/*.md", docs/**]
+  workflow_dispatch:
+  workflow_call: # make this workflow reusable by release.yml
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    # prevent this action from running on forks
+    if: github.repository == 'abinit/abipy'
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - os: ubuntu-latest
+            python: "3.11"
+          - os: ubuntu-latest
+            python: "3.12"
+
+    runs-on: ${{ matrix.config.os }}
+
+    env:
+      PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
+
+    steps:
+      - name: Checkout Abipy repo
+        uses: actions/checkout@v4
+
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+            auto-update-conda: true
+
+      - name: Installing abinit from conda-forge and abipy with python=${{ matrix.config.python }}
+        run: |
+            conda create -n abipy python=${{ matrix.config.python }} --yes
+            conda activate abipy
+            conda install abinit -c conda-forge --yes
+            mpirun -n 1 abinit --version
+            mpirun -n 1 abinit --build
+            pip install -r requirements.txt
+            pip install -r requirements-optional.txt
+            pip install -r requirements-panel.txt
+            pip install --editable .
+            mkdir -p $HOME/.abinit/abipy/
+            cp abipy/data/managers/gh_manager.yml $HOME/.abinit/abipy/manager.yml
+            cp abipy/data/managers/gh_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
+
+      - name: pytest
+        run: |
+          conda activate abipy
+          pip install -r requirements-tests.txt
+          pytest -v .
+
+      - name: integration_tests
+        run: |
+          conda activate abipy
+          abicheck.py --with-flow
+          pytest -v abipy/integration_tests

.gitignore

@@ -52,6 +52,9 @@ docs/flow_gallery
 # Pycharm
 .idea/
 
+# VSC
+.vscode/
+
 # vim files
 *.swp
 *.swo

.travis.yml

@@ -3,17 +3,16 @@ language: python
 
 env:
   global:
-  - ABINIT_VERSION=8.10.1
+  - ABINIT_VERSION=9.0.4
   - ABIPY_PYTEST=yes
+  - ABIPY_SPHINX=no
+  - ABIPY_INSTALLER=pip
+  - ABIPY_COVERALLS=no
   - OPENBLAS_NUM_THREADS=1
   - OMP_NUM_THREADS=1
 
 matrix:
   include:
-    - os: linux
-      python: 3.6
-      env:
-        - ABIPY_INSTALLER=pip ABIPY_PYTEST=no
     - os: linux
       python: 3.7
       dist: xenial
@@ -25,10 +24,15 @@ matrix:
       sudo: true
       env:
         - ABIPY_INSTALLER=conda ABIPY_SPHINX=yes
-#- os: linux
-#  python: 3.8
-#  env:
-#    - ABIPY_INSTALLER=conda ABIPY_PYTEST=no
+    - os: linux
+      python: 3.8
+      env:
+        - ABIPY_INSTALLER=conda ABIPY_PYTEST=no
+    - os: linux
+      python: 3.9
+      env:
+        - ABIPY_INSTALLER=pip ABIPY_SPHINX=yes ABIPY_COVERALLS=yes
+
 
 install:
   #- set -ev  # exit on first error, print each command
@@ -55,7 +59,6 @@ install:
         conda uninstall -y pymatgen
       fi
 
-  - if [[ "${TRAVIS_PYTHON_VERSION}" == "2.7" ]]; then conda install mock; fi
   - pip install coverage>=4.4 -U --upgrade-strategy=eager
 
   # Mayavi (optional requirement)

CHANGELOG.rst

@@ -1,4 +1,76 @@
-Release 0.8.0: xxxx-xx-xx
+Release 0.9.8:
+
+    * Support for python 3.12, scipy 1.14 and numpy 2.0
+    * Compatibility with pymatgen v2024.9.10
+    * Abipy can now read magmoms from the GSR file
+    * Workflows and post-processing tools for photoluminescence calculations.
+    * Additional tools for post-processing E-PH calculations.
+
+Release 0.9.6:
+
+    * Version compatible with aiida-common-workflows.
+
+Release 0.9.5:
+
+    * Force make_dte_inputs to consider the psp to be in LDA
+    * Fix ngfft issue when going to DTE
+    * Force DTE to overwrite nband and nbdbuf to number of VBs and 0 respectively
+
+Release 0.9.4:
+
+    * pymatgen == 2023.7.17 is highly recommended.
+
+Release 0.9.3:
+
+    * Require pymatgen >= 2023.3.23
+    * Add ``ndivsm`` argument to PhononWork and EffMassLineWork to activate band 
+      structure computation along k-path.
+    * Add new option to TaskManager (`limits_for_task_class`) to specify custom limits 
+      depending on the name of the task class. See `abidoc.py manager` for syntax
+    * Deprecate `single` and `rapid` commands of abirun.py.
+
+
+Release 0.9.2:
+
+   * Require pymatgen >= 2022.0.14
+   * Add abiview.py ifermi_fs
+   * G0W0WithQptdmFlow is deprecated and will be removed in v 0.9.3
+   * Add abigui.py script
+   * Add abilab.abirobot function to create a Robot from a list of filepaths.
+   * Add plotly version of fatbands
+   * Support for dipquad and quadquad
+
+Release 0.9.1:
+
+   * Add  "-ew", "--expose-web",
+   * abiopen, abiview and abicomp now supports --plotly to produce plotly figures in the local browser
+     and --chart-studio to push the figure to the chart studio service.
+     Note that, at present, only DDB files support plotly.
+   * AbinitInput set_kpath and make_ebands_input now support negative values of ndivsm that
+     are interpreted as line_density following pymatgen conventions.
+     This option is the recommended one if the k-path contains two consecutive high symmetry k-points
+     that are very close as ndivsm > 0 may produce a very large number of wavevectors.
+   * Preliminary support for plotly plots (phonons).
+   * AbinitInputParser now can parse strings in the input file and read structure is the `structure:abivars`
+     syntax in used.
+
+Release 0.9.0:
+
+    * Require pymatgen >= 2019.12.22
+    * Integration with abinit 9.4.0
+    * Support for py3.8 and py3.9
+    * Converters for phonopy and tdep.
+    * Preliminary support for panel dashboards.
+    * Introduce ABIPY_TMPDIR environment variable to specify the workdir of the temporary tasks at runtime.
+    * Use last version of apscheduler.
+    * Minor bug fixes
+    * New tools for Phonon and EPH calculations.
+    * Note that this is the last AbiPy version supporting Abinit8.
+      AbiPy version 1.0 will start to take advantage of features and ameliorations introduced in Abinit9
+      We will also take the opportunity to refactor the code base so backward incompatibe changes in the API
+      are expected in the next major version.
+
+Release 0.8.0:
 
     * Add abicheck.py --create-config option to install predefined yaml configuration files
     * Add support for NSCF calculations with meta-GGA.
@@ -38,7 +110,7 @@ Release:0.3.0 2017-12-26
       and ``flow-gallery`` with AbiPy flows are now automatically generated.
     * Add Shankland-Koelling-Wood Fourier interpolation scheme.
 
-Release 0.2.0 <2017-03-10>
+Release 0.2.0 2017-03-10
 
     This is the first official release in which we have reached a relatively stable API
     and a well-defined interface with the netcdf files produced by Abinit.